Starting phenix.real_space_refine on Sat Dec 16 08:23:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7teo_25848/12_2023/7teo_25848.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7teo_25848/12_2023/7teo_25848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7teo_25848/12_2023/7teo_25848.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7teo_25848/12_2023/7teo_25848.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7teo_25848/12_2023/7teo_25848.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7teo_25848/12_2023/7teo_25848.pdb" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.115 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 162 5.16 5 C 30952 2.51 5 N 8304 2.21 5 O 9492 1.98 5 H 48612 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 GLU 121": "OE1" <-> "OE2" Residue "B ASP 87": "OD1" <-> "OD2" Residue "B PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 207": "OD1" <-> "OD2" Residue "D ASP 68": "OD1" <-> "OD2" Residue "D ASP 142": "OD1" <-> "OD2" Residue "D ASP 180": "OD1" <-> "OD2" Residue "D TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 71": "OD1" <-> "OD2" Residue "E PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 146": "OE1" <-> "OE2" Residue "G ASP 17": "OD1" <-> "OD2" Residue "H GLU 103": "OE1" <-> "OE2" Residue "H ASP 123": "OD1" <-> "OD2" Residue "H GLU 169": "OE1" <-> "OE2" Residue "I TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 179": "OE1" <-> "OE2" Residue "I ASP 212": "OD1" <-> "OD2" Residue "I GLU 227": "OE1" <-> "OE2" Residue "J ASP 144": "OD1" <-> "OD2" Residue "K GLU 49": "OE1" <-> "OE2" Residue "K GLU 58": "OE1" <-> "OE2" Residue "K GLU 87": "OE1" <-> "OE2" Residue "K TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 169": "OE1" <-> "OE2" Residue "L ASP 92": "OD1" <-> "OD2" Residue "L GLU 147": "OE1" <-> "OE2" Residue "L GLU 257": "OE1" <-> "OE2" Residue "L ASP 267": "OD1" <-> "OD2" Residue "M ASP 45": "OD1" <-> "OD2" Residue "M PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ASP 87": "OD1" <-> "OD2" Residue "Q GLU 237": "OE1" <-> "OE2" Residue "R TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ASP 180": "OD1" <-> "OD2" Residue "S PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S GLU 110": "OE1" <-> "OE2" Residue "T TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U ASP 233": "OD1" <-> "OD2" Residue "U ASP 240": "OD1" <-> "OD2" Residue "V GLU 83": "OE1" <-> "OE2" Residue "W GLU 93": "OE1" <-> "OE2" Residue "W TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W GLU 179": "OE1" <-> "OE2" Residue "W ASP 212": "OD1" <-> "OD2" Residue "X GLU 65": "OE1" <-> "OE2" Residue "X ASP 178": "OD1" <-> "OD2" Residue "Y ASP 72": "OD1" <-> "OD2" Residue "Y GLU 155": "OE1" <-> "OE2" Residue "Y GLU 169": "OE1" <-> "OE2" Residue "Z GLU 111": "OE1" <-> "OE2" Residue "Z GLU 131": "OE1" <-> "OE2" Residue "Z GLU 145": "OE1" <-> "OE2" Residue "Z TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z GLU 257": "OE1" <-> "OE2" Residue "Z ASP 267": "OD1" <-> "OD2" Residue "a GLU 132": "OE1" <-> "OE2" Residue "a ASP 201": "OD1" <-> "OD2" Residue "a PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 132": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 97522 Number of models: 1 Model: "" Number of chains: 30 Chain: "1" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 3449 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 213} Chain: "2" Number of atoms: 3595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3595 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 8, 'TRANS': 221} Chain: "A" Number of atoms: 3687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 3687 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 10, 'TRANS': 223} Chain breaks: 1 Chain: "B" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 3694 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 228} Chain: "C" Number of atoms: 3521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 3521 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain breaks: 4 Chain: "D" Number of atoms: 3288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 3288 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 8, 'TRANS': 199} Chain breaks: 2 Chain: "E" Number of atoms: 3176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3176 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 3, 'TRANS': 203} Chain breaks: 2 Chain: "F" Number of atoms: 3551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3551 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain: "G" Number of atoms: 3776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 3776 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 9, 'TRANS': 233} Chain: "H" Number of atoms: 2992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 2992 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 191} Chain: "I" Number of atoms: 3347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3347 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 6, 'TRANS': 213} Chain: "J" Number of atoms: 3142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 3142 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 195} Chain: "K" Number of atoms: 3130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 3130 Classifications: {'peptide': 195} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain: "L" Number of atoms: 3237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3237 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 209} Chain: "M" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 3449 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 213} Chain: "N" Number of atoms: 3595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3595 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 8, 'TRANS': 221} Chain: "O" Number of atoms: 3687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 3687 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 10, 'TRANS': 223} Chain breaks: 1 Chain: "P" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 3694 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 228} Chain: "Q" Number of atoms: 3521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 3521 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain breaks: 4 Chain: "R" Number of atoms: 3287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 3287 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 8, 'TRANS': 199} Chain breaks: 2 Chain: "S" Number of atoms: 3176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3176 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 3, 'TRANS': 203} Chain breaks: 2 Chain: "T" Number of atoms: 3551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3551 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain: "U" Number of atoms: 3776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 3776 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 9, 'TRANS': 233} Chain: "V" Number of atoms: 2991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 2991 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 191} Chain: "W" Number of atoms: 3347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3347 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 6, 'TRANS': 213} Chain: "X" Number of atoms: 3142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 3142 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 195} Chain: "Y" Number of atoms: 3130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 3130 Classifications: {'peptide': 195} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain: "Z" Number of atoms: 3237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3237 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 209} Chain: "a" Number of atoms: 1177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1177 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 14, 'TRANS': 66} Chain breaks: 3 Chain: "b" Number of atoms: 1177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1177 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 14, 'TRANS': 66} Chain breaks: 3 Time building chain proxies: 32.02, per 1000 atoms: 0.33 Number of scatterers: 97522 At special positions: 0 Unit cell: (187.62, 198.22, 144.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 162 16.00 O 9492 8.00 N 8304 7.00 C 30952 6.00 H 48612 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 61.83 Conformation dependent library (CDL) restraints added in 7.9 seconds 12360 Ramachandran restraints generated. 6180 Oldfield, 0 Emsley, 6180 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11564 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 72 sheets defined 40.1% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.43 Creating SS restraints... Processing helix chain '1' and resid 76 through 98 Processing helix chain '1' and resid 104 through 118 Processing helix chain '1' and resid 161 through 174 Proline residue: 1 167 - end of helix Processing helix chain '1' and resid 195 through 214 Processing helix chain '2' and resid 90 through 108 removed outlier: 3.654A pdb=" N ALA 2 108 " --> pdb=" O VAL 2 104 " (cutoff:3.500A) Processing helix chain '2' and resid 121 through 139 Processing helix chain '2' and resid 178 through 182 Processing helix chain '2' and resid 183 through 192 removed outlier: 4.182A pdb=" N LEU 2 187 " --> pdb=" O MET 2 183 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL 2 191 " --> pdb=" O LEU 2 187 " (cutoff:3.500A) Processing helix chain '2' and resid 194 through 198 Processing helix chain '2' and resid 202 through 221 Processing helix chain '2' and resid 252 through 258 removed outlier: 3.847A pdb=" N LYS 2 256 " --> pdb=" O ASP 2 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 34 Processing helix chain 'A' and resid 35 through 37 No H-bonds generated for 'chain 'A' and resid 35 through 37' Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 86 through 109 Processing helix chain 'A' and resid 113 through 131 Processing helix chain 'A' and resid 174 through 188 Processing helix chain 'A' and resid 198 through 215 removed outlier: 3.582A pdb=" N VAL A 202 " --> pdb=" O SER A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 250 Processing helix chain 'B' and resid 18 through 30 removed outlier: 3.827A pdb=" N ASP B 22 " --> pdb=" O LEU B 18 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TYR B 23 " --> pdb=" O GLY B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 61 Processing helix chain 'B' and resid 78 through 96 Processing helix chain 'B' and resid 97 through 102 Processing helix chain 'B' and resid 106 through 123 removed outlier: 3.859A pdb=" N ALA B 121 " --> pdb=" O ILE B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 179 Processing helix chain 'B' and resid 184 through 200 Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 239 through 250 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 78 through 100 removed outlier: 3.526A pdb=" N SER C 82 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG C 83 " --> pdb=" O ASN C 79 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 123 removed outlier: 3.812A pdb=" N TYR C 120 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR C 121 " --> pdb=" O GLN C 117 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN C 122 " --> pdb=" O GLN C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 178 removed outlier: 3.663A pdb=" N GLU C 173 " --> pdb=" O LYS C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 201 Processing helix chain 'C' and resid 225 through 243 removed outlier: 3.690A pdb=" N GLN C 231 " --> pdb=" O GLU C 227 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR C 232 " --> pdb=" O GLU C 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 28 Processing helix chain 'D' and resid 78 through 100 removed outlier: 4.526A pdb=" N ILE D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 120 removed outlier: 3.956A pdb=" N TYR D 120 " --> pdb=" O VAL D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 177 removed outlier: 3.576A pdb=" N LYS D 177 " --> pdb=" O GLU D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 200 Processing helix chain 'D' and resid 205 through 208 removed outlier: 3.609A pdb=" N LYS D 208 " --> pdb=" O THR D 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 205 through 208' Processing helix chain 'D' and resid 225 through 241 removed outlier: 3.665A pdb=" N TYR D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU D 239 " --> pdb=" O GLN D 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 64 Processing helix chain 'E' and resid 82 through 104 Processing helix chain 'E' and resid 108 through 118 Processing helix chain 'E' and resid 175 through 187 removed outlier: 4.718A pdb=" N ALA E 181 " --> pdb=" O GLU E 177 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU E 182 " --> pdb=" O GLY E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 207 Processing helix chain 'E' and resid 232 through 248 Processing helix chain 'F' and resid 19 through 32 removed outlier: 3.933A pdb=" N ALA F 25 " --> pdb=" O GLN F 21 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS F 30 " --> pdb=" O LEU F 26 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY F 32 " --> pdb=" O ALA F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 100 Processing helix chain 'F' and resid 104 through 120 removed outlier: 4.013A pdb=" N ASN F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR F 120 " --> pdb=" O ALA F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 180 removed outlier: 4.414A pdb=" N ALA F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ASP F 177 " --> pdb=" O GLU F 173 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N THR F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 198 Processing helix chain 'F' and resid 227 through 232 removed outlier: 4.130A pdb=" N LYS F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 31 Processing helix chain 'G' and resid 80 through 102 Processing helix chain 'G' and resid 107 through 122 Processing helix chain 'G' and resid 167 through 182 Processing helix chain 'G' and resid 187 through 205 removed outlier: 3.616A pdb=" N LYS G 193 " --> pdb=" O ARG G 189 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASP G 205 " --> pdb=" O LEU G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 247 Processing helix chain 'H' and resid 67 through 90 Processing helix chain 'H' and resid 93 through 108 Processing helix chain 'H' and resid 147 through 152 removed outlier: 3.895A pdb=" N THR H 151 " --> pdb=" O SER H 148 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE H 152 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 161 Processing helix chain 'H' and resid 166 through 185 Processing helix chain 'H' and resid 208 through 213 Processing helix chain 'I' and resid 78 through 100 Processing helix chain 'I' and resid 104 through 119 removed outlier: 3.680A pdb=" N TYR I 119 " --> pdb=" O HIS I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 171 removed outlier: 3.546A pdb=" N VAL I 166 " --> pdb=" O ALA I 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 195 Processing helix chain 'J' and resid 4 through 8 removed outlier: 4.710A pdb=" N ASN J 8 " --> pdb=" O PRO J 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 4 through 8' Processing helix chain 'J' and resid 56 through 79 Processing helix chain 'J' and resid 83 through 97 Processing helix chain 'J' and resid 142 through 154 Processing helix chain 'J' and resid 159 through 176 Processing helix chain 'K' and resid 49 through 72 removed outlier: 3.970A pdb=" N VAL K 54 " --> pdb=" O ALA K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 93 removed outlier: 4.375A pdb=" N ARG K 93 " --> pdb=" O ALA K 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 148 removed outlier: 3.860A pdb=" N TYR K 139 " --> pdb=" O TYR K 135 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR K 140 " --> pdb=" O SER K 136 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N SER K 142 " --> pdb=" O PHE K 138 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU K 143 " --> pdb=" O TYR K 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 172 Processing helix chain 'L' and resid 123 through 146 Processing helix chain 'L' and resid 150 through 165 Processing helix chain 'L' and resid 207 through 219 removed outlier: 3.795A pdb=" N SER L 217 " --> pdb=" O GLY L 213 " (cutoff:3.500A) Processing helix chain 'L' and resid 224 through 243 Processing helix chain 'L' and resid 268 through 280 removed outlier: 4.795A pdb=" N TRP L 273 " --> pdb=" O GLY L 269 " (cutoff:3.500A) Processing helix chain 'M' and resid 76 through 98 Processing helix chain 'M' and resid 104 through 118 Processing helix chain 'M' and resid 161 through 174 Proline residue: M 167 - end of helix Processing helix chain 'M' and resid 195 through 214 Processing helix chain 'N' and resid 90 through 108 Processing helix chain 'N' and resid 121 through 139 Processing helix chain 'N' and resid 178 through 182 Processing helix chain 'N' and resid 183 through 192 removed outlier: 4.327A pdb=" N LEU N 187 " --> pdb=" O MET N 183 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL N 191 " --> pdb=" O LEU N 187 " (cutoff:3.500A) Processing helix chain 'N' and resid 194 through 198 Processing helix chain 'N' and resid 202 through 221 Processing helix chain 'N' and resid 252 through 258 removed outlier: 3.822A pdb=" N LYS N 256 " --> pdb=" O ASP N 253 " (cutoff:3.500A) Processing helix chain 'O' and resid 25 through 34 Processing helix chain 'O' and resid 35 through 37 No H-bonds generated for 'chain 'O' and resid 35 through 37' Processing helix chain 'O' and resid 65 through 69 Processing helix chain 'O' and resid 86 through 109 Processing helix chain 'O' and resid 113 through 131 Processing helix chain 'O' and resid 174 through 188 removed outlier: 3.553A pdb=" N ILE O 178 " --> pdb=" O LYS O 174 " (cutoff:3.500A) Processing helix chain 'O' and resid 198 through 215 Processing helix chain 'O' and resid 237 through 250 Processing helix chain 'P' and resid 20 through 30 Processing helix chain 'P' and resid 57 through 61 Processing helix chain 'P' and resid 78 through 96 Processing helix chain 'P' and resid 97 through 102 Processing helix chain 'P' and resid 106 through 123 removed outlier: 3.831A pdb=" N ALA P 121 " --> pdb=" O ILE P 117 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 179 removed outlier: 3.574A pdb=" N LYS P 177 " --> pdb=" O THR P 173 " (cutoff:3.500A) Processing helix chain 'P' and resid 184 through 200 Processing helix chain 'P' and resid 218 through 222 Processing helix chain 'P' and resid 239 through 250 Processing helix chain 'Q' and resid 12 through 16 removed outlier: 4.260A pdb=" N HIS Q 16 " --> pdb=" O PRO Q 13 " (cutoff:3.500A) Processing helix chain 'Q' and resid 17 through 29 Processing helix chain 'Q' and resid 78 through 100 removed outlier: 3.659A pdb=" N ARG Q 83 " --> pdb=" O ASN Q 79 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE Q 84 " --> pdb=" O ALA Q 80 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG Q 97 " --> pdb=" O ALA Q 93 " (cutoff:3.500A) Processing helix chain 'Q' and resid 105 through 123 removed outlier: 3.731A pdb=" N TYR Q 120 " --> pdb=" O VAL Q 116 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR Q 121 " --> pdb=" O GLN Q 117 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN Q 122 " --> pdb=" O GLN Q 118 " (cutoff:3.500A) Processing helix chain 'Q' and resid 167 through 178 removed outlier: 4.814A pdb=" N GLU Q 173 " --> pdb=" O LYS Q 169 " (cutoff:3.500A) Processing helix chain 'Q' and resid 187 through 202 Processing helix chain 'Q' and resid 225 through 243 Processing helix chain 'R' and resid 19 through 28 Processing helix chain 'R' and resid 78 through 100 removed outlier: 4.486A pdb=" N ILE R 84 " --> pdb=" O ALA R 80 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU R 85 " --> pdb=" O ASP R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 120 removed outlier: 3.755A pdb=" N TYR R 120 " --> pdb=" O VAL R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 177 removed outlier: 3.511A pdb=" N LYS R 177 " --> pdb=" O GLU R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 200 Processing helix chain 'R' and resid 205 through 209 Processing helix chain 'R' and resid 225 through 241 removed outlier: 3.861A pdb=" N GLU R 239 " --> pdb=" O GLN R 235 " (cutoff:3.500A) Processing helix chain 'S' and resid 60 through 64 Processing helix chain 'S' and resid 82 through 104 Processing helix chain 'S' and resid 108 through 118 Processing helix chain 'S' and resid 175 through 187 removed outlier: 4.709A pdb=" N ALA S 181 " --> pdb=" O GLU S 177 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU S 182 " --> pdb=" O GLY S 178 " (cutoff:3.500A) Processing helix chain 'S' and resid 192 through 208 removed outlier: 3.515A pdb=" N LEU S 198 " --> pdb=" O LYS S 194 " (cutoff:3.500A) Processing helix chain 'S' and resid 232 through 248 Processing helix chain 'T' and resid 19 through 32 removed outlier: 3.645A pdb=" N ALA T 25 " --> pdb=" O GLN T 21 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY T 32 " --> pdb=" O ALA T 28 " (cutoff:3.500A) Processing helix chain 'T' and resid 77 through 100 Processing helix chain 'T' and resid 104 through 120 removed outlier: 3.526A pdb=" N LYS T 118 " --> pdb=" O ASP T 114 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASN T 119 " --> pdb=" O LYS T 115 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR T 120 " --> pdb=" O ALA T 116 " (cutoff:3.500A) Processing helix chain 'T' and resid 164 through 180 removed outlier: 4.366A pdb=" N ALA T 168 " --> pdb=" O ARG T 164 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ASP T 177 " --> pdb=" O GLU T 173 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N THR T 178 " --> pdb=" O ARG T 174 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE T 180 " --> pdb=" O LEU T 176 " (cutoff:3.500A) Processing helix chain 'T' and resid 186 through 198 Processing helix chain 'T' and resid 199 through 201 No H-bonds generated for 'chain 'T' and resid 199 through 201' Processing helix chain 'T' and resid 228 through 233 removed outlier: 3.964A pdb=" N LYS T 232 " --> pdb=" O ALA T 229 " (cutoff:3.500A) Processing helix chain 'U' and resid 20 through 31 Processing helix chain 'U' and resid 80 through 102 Processing helix chain 'U' and resid 107 through 122 Processing helix chain 'U' and resid 167 through 182 Processing helix chain 'U' and resid 187 through 204 removed outlier: 3.803A pdb=" N LYS U 193 " --> pdb=" O ARG U 189 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU U 204 " --> pdb=" O TYR U 200 " (cutoff:3.500A) Processing helix chain 'U' and resid 205 through 207 No H-bonds generated for 'chain 'U' and resid 205 through 207' Processing helix chain 'U' and resid 231 through 247 Processing helix chain 'V' and resid 67 through 90 Processing helix chain 'V' and resid 93 through 108 Processing helix chain 'V' and resid 149 through 152 Processing helix chain 'V' and resid 153 through 161 Processing helix chain 'V' and resid 166 through 185 Processing helix chain 'V' and resid 208 through 213 Processing helix chain 'W' and resid 78 through 100 Processing helix chain 'W' and resid 104 through 119 removed outlier: 3.659A pdb=" N TYR W 119 " --> pdb=" O HIS W 115 " (cutoff:3.500A) Processing helix chain 'W' and resid 159 through 171 Processing helix chain 'W' and resid 176 through 195 Processing helix chain 'X' and resid 4 through 8 removed outlier: 4.597A pdb=" N ASN X 8 " --> pdb=" O PRO X 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 4 through 8' Processing helix chain 'X' and resid 56 through 79 Processing helix chain 'X' and resid 83 through 97 Processing helix chain 'X' and resid 142 through 154 Processing helix chain 'X' and resid 159 through 176 Processing helix chain 'Y' and resid 49 through 72 removed outlier: 3.949A pdb=" N VAL Y 54 " --> pdb=" O ALA Y 50 " (cutoff:3.500A) Processing helix chain 'Y' and resid 76 through 93 removed outlier: 4.419A pdb=" N ARG Y 93 " --> pdb=" O ALA Y 89 " (cutoff:3.500A) Processing helix chain 'Y' and resid 135 through 148 removed outlier: 3.919A pdb=" N TYR Y 139 " --> pdb=" O TYR Y 135 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N SER Y 142 " --> pdb=" O PHE Y 138 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU Y 143 " --> pdb=" O TYR Y 139 " (cutoff:3.500A) Processing helix chain 'Y' and resid 153 through 172 Processing helix chain 'Z' and resid 123 through 146 Processing helix chain 'Z' and resid 150 through 165 Processing helix chain 'Z' and resid 207 through 219 removed outlier: 3.570A pdb=" N VAL Z 214 " --> pdb=" O PHE Z 210 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER Z 217 " --> pdb=" O GLY Z 213 " (cutoff:3.500A) Processing helix chain 'Z' and resid 224 through 243 Processing helix chain 'Z' and resid 268 through 280 removed outlier: 4.826A pdb=" N TRP Z 273 " --> pdb=" O GLY Z 269 " (cutoff:3.500A) Processing helix chain 'a' and resid 152 through 155 Processing helix chain 'a' and resid 156 through 161 Processing helix chain 'a' and resid 167 through 172 Processing helix chain 'a' and resid 209 through 213 Processing helix chain 'b' and resid 152 through 155 Processing helix chain 'b' and resid 156 through 161 Processing helix chain 'b' and resid 167 through 172 Processing sheet with id=AA1, first strand: chain '1' and resid 155 through 159 removed outlier: 5.295A pdb=" N THR 1 30 " --> pdb=" O ASP 1 45 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE 1 39 " --> pdb=" O GLY 1 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '1' and resid 48 through 50 removed outlier: 6.846A pdb=" N ASN 1 48 " --> pdb=" O ASN 1 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '1' and resid 62 through 64 removed outlier: 3.695A pdb=" N ASN 1 74 " --> pdb=" O HIS 1 127 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR 1 128 " --> pdb=" O PHE 1 144 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL 1 141 " --> pdb=" O GLU 1 153 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP 1 145 " --> pdb=" O SER 1 149 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N SER 1 149 " --> pdb=" O ASP 1 145 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 66 through 69 removed outlier: 5.341A pdb=" N LEU 2 67 " --> pdb=" O TYR 2 63 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TYR 2 63 " --> pdb=" O LEU 2 67 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N THR 2 82 " --> pdb=" O VAL 2 78 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '2' and resid 66 through 69 removed outlier: 5.341A pdb=" N LEU 2 67 " --> pdb=" O TYR 2 63 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TYR 2 63 " --> pdb=" O LEU 2 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '2' and resid 174 through 176 removed outlier: 5.699A pdb=" N PHE 2 228 " --> pdb=" O ASN 2 244 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN 2 244 " --> pdb=" O PHE 2 228 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 168 through 171 Processing sheet with id=AA8, first strand: chain 'A' and resid 72 through 74 Processing sheet with id=AA9, first strand: chain 'B' and resid 161 through 164 removed outlier: 3.711A pdb=" N GLY B 42 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LEU B 211 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 65 through 68 removed outlier: 5.612A pdb=" N LEU B 66 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ALA B 73 " --> pdb=" O LEU B 66 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 224 through 225 removed outlier: 6.303A pdb=" N THR B 225 " --> pdb=" O TYR I 215 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG I 217 " --> pdb=" O THR B 225 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ASP I 212 " --> pdb=" O GLU I 208 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N GLU I 208 " --> pdb=" O ASP I 212 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN I 218 " --> pdb=" O VAL I 202 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N VAL I 202 " --> pdb=" O ASN I 218 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 161 through 164 Processing sheet with id=AB4, first strand: chain 'C' and resid 65 through 68 removed outlier: 6.685A pdb=" N VAL C 71 " --> pdb=" O ILE C 67 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY C 137 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS C 146 " --> pdb=" O GLY C 137 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE C 155 " --> pdb=" O GLU C 151 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 161 through 164 Processing sheet with id=AB6, first strand: chain 'D' and resid 65 through 68 removed outlier: 6.614A pdb=" N VAL D 71 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 169 through 172 Processing sheet with id=AB8, first strand: chain 'E' and resid 67 through 71 removed outlier: 5.972A pdb=" N ILE E 67 " --> pdb=" O MET E 78 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N MET E 78 " --> pdb=" O ILE E 67 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLU E 69 " --> pdb=" O CYS E 76 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N CYS E 76 " --> pdb=" O GLU E 69 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N LEU E 142 " --> pdb=" O ALA E 158 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA E 158 " --> pdb=" O LEU E 142 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 158 through 161 removed outlier: 5.792A pdb=" N GLY F 217 " --> pdb=" O PRO F 221 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 63 through 67 removed outlier: 6.255A pdb=" N MET F 70 " --> pdb=" O CYS F 66 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 161 through 164 removed outlier: 3.623A pdb=" N GLY G 44 " --> pdb=" O CYS G 41 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 67 through 69 Processing sheet with id=AC4, first strand: chain 'H' and resid 143 through 146 Processing sheet with id=AC5, first strand: chain 'H' and resid 39 through 41 removed outlier: 7.027A pdb=" N THR H 39 " --> pdb=" O ALA H 46 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 53 through 57 removed outlier: 6.481A pdb=" N ILE H 60 " --> pdb=" O VAL H 56 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 49 through 51 removed outlier: 6.377A pdb=" N GLN I 51 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N VAL I 55 " --> pdb=" O GLN I 51 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 64 through 67 removed outlier: 6.161A pdb=" N ILE I 70 " --> pdb=" O ILE I 66 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 64 through 67 removed outlier: 6.161A pdb=" N ILE I 70 " --> pdb=" O ILE I 66 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 241 through 246 removed outlier: 6.554A pdb=" N TYR J 199 " --> pdb=" O LEU I 242 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLU I 244 " --> pdb=" O LYS J 197 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LYS J 197 " --> pdb=" O GLU I 244 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ILE I 246 " --> pdb=" O VAL J 195 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL J 195 " --> pdb=" O ILE I 246 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA J 185 " --> pdb=" O LEU J 200 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ILE J 11 " --> pdb=" O ASP J 26 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 29 through 31 removed outlier: 6.611A pdb=" N LEU J 29 " --> pdb=" O VAL J 36 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 43 through 46 removed outlier: 3.674A pdb=" N VAL J 49 " --> pdb=" O TYR J 46 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 130 through 132 removed outlier: 4.643A pdb=" N VAL K 181 " --> pdb=" O VAL K 192 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 21 through 23 removed outlier: 6.630A pdb=" N ARG K 23 " --> pdb=" O VAL K 27 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N VAL K 27 " --> pdb=" O ARG K 23 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 35 through 39 removed outlier: 6.408A pdb=" N THR K 42 " --> pdb=" O LEU K 38 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 201 through 204 removed outlier: 3.989A pdb=" N GLY L 264 " --> pdb=" O LEU L 252 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N HIS L 254 " --> pdb=" O TYR L 262 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N TYR L 262 " --> pdb=" O HIS L 254 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N THR L 256 " --> pdb=" O TRP L 260 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N TRP L 260 " --> pdb=" O THR L 256 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 95 through 97 removed outlier: 6.856A pdb=" N ALA L 95 " --> pdb=" O ALA L 102 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 109 through 113 removed outlier: 6.411A pdb=" N LEU L 116 " --> pdb=" O ILE L 112 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'M' and resid 155 through 159 removed outlier: 5.327A pdb=" N THR M 30 " --> pdb=" O ASP M 45 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 48 through 50 removed outlier: 6.734A pdb=" N ASN M 48 " --> pdb=" O ASN M 55 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 63 through 64 removed outlier: 3.617A pdb=" N ASN M 74 " --> pdb=" O HIS M 127 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL M 141 " --> pdb=" O GLU M 153 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 66 through 69 removed outlier: 5.382A pdb=" N LEU N 67 " --> pdb=" O TYR N 63 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TYR N 63 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N THR N 82 " --> pdb=" O VAL N 78 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 66 through 69 removed outlier: 5.382A pdb=" N LEU N 67 " --> pdb=" O TYR N 63 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TYR N 63 " --> pdb=" O LEU N 67 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 174 through 176 removed outlier: 5.738A pdb=" N PHE N 228 " --> pdb=" O ASN N 244 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN N 244 " --> pdb=" O PHE N 228 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'O' and resid 168 through 171 Processing sheet with id=AE8, first strand: chain 'O' and resid 72 through 74 Processing sheet with id=AE9, first strand: chain 'P' and resid 161 through 164 removed outlier: 3.575A pdb=" N GLY P 42 " --> pdb=" O ALA P 39 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU P 211 " --> pdb=" O LEU P 238 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'P' and resid 65 through 68 removed outlier: 6.479A pdb=" N ILE P 71 " --> pdb=" O LEU P 67 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P' and resid 224 through 225 removed outlier: 6.250A pdb=" N THR P 225 " --> pdb=" O TYR W 215 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ARG W 217 " --> pdb=" O THR P 225 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ASP W 212 " --> pdb=" O GLU W 208 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N GLU W 208 " --> pdb=" O ASP W 212 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN W 218 " --> pdb=" O VAL W 202 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N VAL W 202 " --> pdb=" O ASN W 218 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Q' and resid 161 through 164 Processing sheet with id=AF4, first strand: chain 'Q' and resid 65 through 66 removed outlier: 3.562A pdb=" N GLY Q 137 " --> pdb=" O LYS Q 146 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU Q 151 " --> pdb=" O ILE Q 155 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ILE Q 155 " --> pdb=" O GLU Q 151 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'R' and resid 161 through 164 removed outlier: 3.504A pdb=" N GLN R 162 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL R 42 " --> pdb=" O VAL R 215 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'R' and resid 65 through 68 removed outlier: 6.729A pdb=" N VAL R 71 " --> pdb=" O ILE R 67 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'S' and resid 169 through 172 Processing sheet with id=AF8, first strand: chain 'S' and resid 67 through 71 removed outlier: 5.820A pdb=" N ILE S 67 " --> pdb=" O MET S 78 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N MET S 78 " --> pdb=" O ILE S 67 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N GLU S 69 " --> pdb=" O CYS S 76 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N CYS S 76 " --> pdb=" O GLU S 69 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N LEU S 142 " --> pdb=" O ALA S 158 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA S 158 " --> pdb=" O LEU S 142 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU S 155 " --> pdb=" O TYR S 167 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'T' and resid 158 through 161 Processing sheet with id=AG1, first strand: chain 'T' and resid 63 through 67 removed outlier: 6.659A pdb=" N MET T 70 " --> pdb=" O CYS T 66 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'U' and resid 161 through 164 Processing sheet with id=AG3, first strand: chain 'U' and resid 67 through 69 Processing sheet with id=AG4, first strand: chain 'V' and resid 143 through 146 Processing sheet with id=AG5, first strand: chain 'V' and resid 39 through 41 removed outlier: 6.462A pdb=" N THR V 41 " --> pdb=" O ILE V 45 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N ILE V 45 " --> pdb=" O THR V 41 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'V' and resid 53 through 57 removed outlier: 6.625A pdb=" N ILE V 60 " --> pdb=" O VAL V 56 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE V 117 " --> pdb=" O CYS V 63 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'W' and resid 49 through 51 removed outlier: 6.271A pdb=" N GLN W 51 " --> pdb=" O VAL W 55 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N VAL W 55 " --> pdb=" O GLN W 51 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'W' and resid 64 through 67 removed outlier: 6.178A pdb=" N ILE W 70 " --> pdb=" O ILE W 66 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'W' and resid 64 through 67 removed outlier: 6.178A pdb=" N ILE W 70 " --> pdb=" O ILE W 66 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'W' and resid 241 through 246 removed outlier: 6.533A pdb=" N TYR X 199 " --> pdb=" O LEU W 242 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLU W 244 " --> pdb=" O LYS X 197 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LYS X 197 " --> pdb=" O GLU W 244 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ILE W 246 " --> pdb=" O VAL X 195 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL X 195 " --> pdb=" O ILE W 246 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA X 185 " --> pdb=" O LEU X 200 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ILE X 11 " --> pdb=" O ASP X 26 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'X' and resid 29 through 31 removed outlier: 6.572A pdb=" N LEU X 29 " --> pdb=" O VAL X 36 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'X' and resid 43 through 46 removed outlier: 3.661A pdb=" N VAL X 49 " --> pdb=" O TYR X 46 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Y' and resid 130 through 132 removed outlier: 4.782A pdb=" N VAL Y 181 " --> pdb=" O VAL Y 192 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'Y' and resid 21 through 23 removed outlier: 6.768A pdb=" N VAL Y 21 " --> pdb=" O LEU Y 28 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'Y' and resid 35 through 39 removed outlier: 6.410A pdb=" N THR Y 42 " --> pdb=" O LEU Y 38 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'Z' and resid 201 through 204 removed outlier: 3.896A pdb=" N GLY Z 264 " --> pdb=" O LEU Z 252 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N HIS Z 254 " --> pdb=" O TYR Z 262 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N TYR Z 262 " --> pdb=" O HIS Z 254 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N THR Z 256 " --> pdb=" O TRP Z 260 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N TRP Z 260 " --> pdb=" O THR Z 256 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'Z' and resid 95 through 97 removed outlier: 6.296A pdb=" N ALA Z 97 " --> pdb=" O VAL Z 101 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N VAL Z 101 " --> pdb=" O ALA Z 97 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'Z' and resid 109 through 113 removed outlier: 6.381A pdb=" N LEU Z 116 " --> pdb=" O ILE Z 112 " (cutoff:3.500A) 2822 hydrogen bonds defined for protein. 7989 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 38.85 Time building geometry restraints manager: 64.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 48536 1.04 - 1.24: 5728 1.24 - 1.44: 15509 1.44 - 1.64: 28399 1.64 - 1.84: 248 Bond restraints: 98420 Sorted by residual: bond pdb=" N PHE 1 21 " pdb=" CA PHE 1 21 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.24e+00 bond pdb=" N HIS O 15 " pdb=" CA HIS O 15 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.20e+00 bond pdb=" N THR P 10 " pdb=" CA THR P 10 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.15e+00 bond pdb=" N PHE D 18 " pdb=" CA PHE D 18 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.08e+00 bond pdb=" N PHE R 18 " pdb=" CA PHE R 18 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 ... (remaining 98415 not shown) Histogram of bond angle deviations from ideal: 99.86 - 106.73: 1299 106.73 - 113.59: 117806 113.59 - 120.46: 31953 120.46 - 127.33: 26352 127.33 - 134.19: 434 Bond angle restraints: 177844 Sorted by residual: angle pdb=" C GLN J 32 " pdb=" CA GLN J 32 " pdb=" CB GLN J 32 " ideal model delta sigma weight residual 117.23 111.58 5.65 1.36e+00 5.41e-01 1.72e+01 angle pdb=" N GLU L 142 " pdb=" CA GLU L 142 " pdb=" CB GLU L 142 " ideal model delta sigma weight residual 110.12 115.88 -5.76 1.47e+00 4.63e-01 1.53e+01 angle pdb=" N GLY 1 218 " pdb=" CA GLY 1 218 " pdb=" C GLY 1 218 " ideal model delta sigma weight residual 113.18 122.33 -9.15 2.37e+00 1.78e-01 1.49e+01 angle pdb=" N GLY M 218 " pdb=" CA GLY M 218 " pdb=" C GLY M 218 " ideal model delta sigma weight residual 113.18 121.95 -8.77 2.37e+00 1.78e-01 1.37e+01 angle pdb=" N VAL D 202 " pdb=" CA VAL D 202 " pdb=" C VAL D 202 " ideal model delta sigma weight residual 113.71 110.30 3.41 9.50e-01 1.11e+00 1.29e+01 ... (remaining 177839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 41518 17.97 - 35.93: 2218 35.93 - 53.90: 686 53.90 - 71.87: 265 71.87 - 89.84: 109 Dihedral angle restraints: 44796 sinusoidal: 23804 harmonic: 20992 Sorted by residual: dihedral pdb=" CA VAL 1 217 " pdb=" C VAL 1 217 " pdb=" N GLY 1 218 " pdb=" CA GLY 1 218 " ideal model delta harmonic sigma weight residual 180.00 -151.18 -28.82 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA VAL M 217 " pdb=" C VAL M 217 " pdb=" N GLY M 218 " pdb=" CA GLY M 218 " ideal model delta harmonic sigma weight residual -180.00 -151.36 -28.64 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA ILE M 165 " pdb=" C ILE M 165 " pdb=" N MET M 166 " pdb=" CA MET M 166 " ideal model delta harmonic sigma weight residual 180.00 -156.41 -23.59 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 44793 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 4745 0.030 - 0.061: 1811 0.061 - 0.091: 495 0.091 - 0.121: 437 0.121 - 0.152: 96 Chirality restraints: 7584 Sorted by residual: chirality pdb=" CA VAL N 44 " pdb=" N VAL N 44 " pdb=" C VAL N 44 " pdb=" CB VAL N 44 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" CA ILE G 136 " pdb=" N ILE G 136 " pdb=" C ILE G 136 " pdb=" CB ILE G 136 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.65e-01 chirality pdb=" CA ILE U 136 " pdb=" N ILE U 136 " pdb=" C ILE U 136 " pdb=" CB ILE U 136 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.33e-01 ... (remaining 7581 not shown) Planarity restraints: 14712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP Q 139 " 0.055 5.00e-02 4.00e+02 8.24e-02 1.09e+01 pdb=" N PRO Q 140 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO Q 140 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO Q 140 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER P 13 " -0.047 5.00e-02 4.00e+02 7.11e-02 8.09e+00 pdb=" N PRO P 14 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO P 14 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO P 14 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY X 106 " 0.047 5.00e-02 4.00e+02 7.10e-02 8.07e+00 pdb=" N PRO X 107 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO X 107 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO X 107 " 0.039 5.00e-02 4.00e+02 ... (remaining 14709 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.11: 2071 2.11 - 2.73: 175068 2.73 - 3.35: 290349 3.35 - 3.98: 380488 3.98 - 4.60: 601850 Nonbonded interactions: 1449826 Sorted by model distance: nonbonded pdb=" O GLY 1 218 " pdb=" H ARG 1 240 " model vdw 1.484 1.850 nonbonded pdb=" O GLY M 218 " pdb=" H ARG M 240 " model vdw 1.524 1.850 nonbonded pdb=" HH TYR K 139 " pdb=" O ILE Y 25 " model vdw 1.539 1.850 nonbonded pdb=" OD1 ASP N 58 " pdb="HH21 ARG N 74 " model vdw 1.540 1.850 nonbonded pdb=" OD1 ASP 2 58 " pdb="HH21 ARG 2 74 " model vdw 1.542 1.850 ... (remaining 1449821 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '1' selection = chain 'M' } ncs_group { reference = chain '2' selection = chain 'N' } ncs_group { reference = chain 'A' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'P' } ncs_group { reference = (chain 'C' and (resid 18 through 48 or resid 62 through 121 or resid 127 through \ 243)) selection = (chain 'D' and (resid 18 through 69 or (resid 70 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name H \ E2)) or resid 71 through 178 or resid 183 through 203 or resid 208 through 243)) \ selection = (chain 'Q' and (resid 18 through 48 or resid 62 through 121 or resid 127 through \ 243)) selection = (chain 'R' and (resid 18 through 178 or resid 183 through 203 or resid 208 throu \ gh 243)) } ncs_group { reference = (chain 'E' and (resid 13 through 98 or (resid 99 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name H \ E1)) or resid 100 through 248)) selection = (chain 'S' and (resid 13 through 187 or (resid 188 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 189 through 248)) } ncs_group { reference = chain 'F' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'U' } ncs_group { reference = (chain 'H' and (resid 20 through 56 or (resid 57 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name H \ E1)) or resid 58 through 215)) selection = chain 'V' } ncs_group { reference = chain 'I' selection = chain 'W' } ncs_group { reference = chain 'J' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'Z' } ncs_group { reference = chain 'a' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 1.010 Extract box with map and model: 13.720 Check model and map are aligned: 1.160 Set scattering table: 0.680 Process input model: 243.330 Find NCS groups from input model: 4.890 Set up NCS constraints: 0.580 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 283.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 49808 Z= 0.185 Angle : 0.548 9.145 67374 Z= 0.311 Chirality : 0.043 0.152 7584 Planarity : 0.004 0.082 8704 Dihedral : 12.701 89.834 18354 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.10), residues: 6180 helix: 1.48 (0.11), residues: 2252 sheet: 0.39 (0.13), residues: 1484 loop : 0.08 (0.13), residues: 2444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP 2 144 HIS 0.010 0.001 HIS T 69 PHE 0.023 0.002 PHE 1 96 TYR 0.026 0.001 TYR M 150 ARG 0.010 0.001 ARG F 82 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12360 Ramachandran restraints generated. 6180 Oldfield, 0 Emsley, 6180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12360 Ramachandran restraints generated. 6180 Oldfield, 0 Emsley, 6180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 774 time to evaluate : 6.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 774 average time/residue: 2.7133 time to fit residues: 2701.3058 Evaluate side-chains 483 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 482 time to evaluate : 6.364 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 7.5767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 523 optimal weight: 2.9990 chunk 469 optimal weight: 5.9990 chunk 260 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 chunk 316 optimal weight: 3.9990 chunk 251 optimal weight: 5.9990 chunk 485 optimal weight: 4.9990 chunk 188 optimal weight: 2.9990 chunk 295 optimal weight: 4.9990 chunk 361 optimal weight: 4.9990 chunk 563 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 99 ASN 1 113 GLN 2 244 ASN B 205 ASN E 73 HIS E 108 ASN E 185 ASN G 126 ASN H 214 GLN K 147 HIS L 128 GLN M 113 GLN O 209 HIS P 241 GLN R 94 GLN S 185 ASN U 61 GLN U 126 ASN U 247 ASN Y 65 GLN Z 128 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 49808 Z= 0.428 Angle : 0.617 9.516 67374 Z= 0.341 Chirality : 0.047 0.186 7584 Planarity : 0.005 0.085 8704 Dihedral : 5.395 50.671 6808 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.93 % Allowed : 7.67 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.10), residues: 6180 helix: 1.43 (0.10), residues: 2282 sheet: 0.20 (0.13), residues: 1494 loop : -0.28 (0.12), residues: 2404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP U 217 HIS 0.008 0.002 HIS 1 114 PHE 0.024 0.002 PHE F 179 TYR 0.024 0.002 TYR M 150 ARG 0.006 0.001 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12360 Ramachandran restraints generated. 6180 Oldfield, 0 Emsley, 6180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12360 Ramachandran restraints generated. 6180 Oldfield, 0 Emsley, 6180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 486 time to evaluate : 6.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 102 outliers final: 44 residues processed: 556 average time/residue: 2.6599 time to fit residues: 1922.5422 Evaluate side-chains 491 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 447 time to evaluate : 6.156 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 27 residues processed: 17 average time/residue: 1.2012 time to fit residues: 40.7967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 312 optimal weight: 2.9990 chunk 174 optimal weight: 0.0980 chunk 468 optimal weight: 2.9990 chunk 383 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 564 optimal weight: 2.9990 chunk 609 optimal weight: 9.9990 chunk 502 optimal weight: 0.9980 chunk 559 optimal weight: 1.9990 chunk 192 optimal weight: 4.9990 chunk 452 optimal weight: 9.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 99 ASN B 205 ASN E 185 ASN K 99 GLN S 185 ASN U 243 GLN Y 99 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 49808 Z= 0.226 Angle : 0.520 8.245 67374 Z= 0.284 Chirality : 0.043 0.166 7584 Planarity : 0.004 0.083 8704 Dihedral : 5.097 41.608 6808 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.46 % Allowed : 8.82 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.10), residues: 6180 helix: 1.71 (0.11), residues: 2290 sheet: 0.18 (0.13), residues: 1490 loop : -0.33 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Z 260 HIS 0.004 0.001 HIS B 94 PHE 0.021 0.001 PHE F 179 TYR 0.014 0.001 TYR Y 73 ARG 0.005 0.000 ARG V 55 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12360 Ramachandran restraints generated. 6180 Oldfield, 0 Emsley, 6180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12360 Ramachandran restraints generated. 6180 Oldfield, 0 Emsley, 6180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 505 time to evaluate : 6.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 43 residues processed: 555 average time/residue: 2.6237 time to fit residues: 1906.4983 Evaluate side-chains 485 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 442 time to evaluate : 6.323 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 27 residues processed: 16 average time/residue: 1.7131 time to fit residues: 48.8235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 557 optimal weight: 3.9990 chunk 424 optimal weight: 7.9990 chunk 292 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 269 optimal weight: 0.5980 chunk 378 optimal weight: 4.9990 chunk 566 optimal weight: 3.9990 chunk 599 optimal weight: 4.9990 chunk 295 optimal weight: 3.9990 chunk 536 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 99 ASN B 205 ASN E 185 ASN K 99 GLN S 185 ASN U 243 GLN Y 99 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 49808 Z= 0.380 Angle : 0.564 7.743 67374 Z= 0.309 Chirality : 0.045 0.166 7584 Planarity : 0.005 0.083 8704 Dihedral : 5.125 33.109 6808 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.10 % Allowed : 9.32 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.10), residues: 6180 helix: 1.69 (0.10), residues: 2292 sheet: -0.03 (0.13), residues: 1462 loop : -0.52 (0.12), residues: 2426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 199 HIS 0.007 0.001 HIS 1 114 PHE 0.021 0.002 PHE F 179 TYR 0.018 0.002 TYR Y 73 ARG 0.004 0.000 ARG T 82 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12360 Ramachandran restraints generated. 6180 Oldfield, 0 Emsley, 6180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12360 Ramachandran restraints generated. 6180 Oldfield, 0 Emsley, 6180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 452 time to evaluate : 6.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 111 outliers final: 53 residues processed: 527 average time/residue: 2.6565 time to fit residues: 1820.5467 Evaluate side-chains 493 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 440 time to evaluate : 6.180 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 36 residues processed: 17 average time/residue: 1.3017 time to fit residues: 42.5847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 499 optimal weight: 4.9990 chunk 340 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 446 optimal weight: 6.9990 chunk 247 optimal weight: 2.9990 chunk 511 optimal weight: 4.9990 chunk 414 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 306 optimal weight: 4.9990 chunk 537 optimal weight: 1.9990 chunk 151 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 99 ASN 2 51 ASN B 205 ASN E 185 ASN I 194 ASN K 99 GLN K 146 HIS S 108 ASN S 185 ASN U 243 GLN Y 99 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 49808 Z= 0.378 Angle : 0.555 6.506 67374 Z= 0.304 Chirality : 0.045 0.164 7584 Planarity : 0.005 0.082 8704 Dihedral : 5.111 32.099 6808 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.15 % Allowed : 10.30 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.10), residues: 6180 helix: 1.75 (0.10), residues: 2280 sheet: -0.11 (0.13), residues: 1440 loop : -0.63 (0.12), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Z 260 HIS 0.010 0.001 HIS O 209 PHE 0.028 0.002 PHE Q 138 TYR 0.017 0.002 TYR W 126 ARG 0.012 0.001 ARG F 51 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12360 Ramachandran restraints generated. 6180 Oldfield, 0 Emsley, 6180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12360 Ramachandran restraints generated. 6180 Oldfield, 0 Emsley, 6180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 475 time to evaluate : 6.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 114 outliers final: 61 residues processed: 551 average time/residue: 2.5976 time to fit residues: 1868.4355 Evaluate side-chains 483 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 422 time to evaluate : 6.121 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 41 residues processed: 20 average time/residue: 1.3958 time to fit residues: 50.5941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 201 optimal weight: 3.9990 chunk 539 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 351 optimal weight: 5.9990 chunk 147 optimal weight: 10.0000 chunk 599 optimal weight: 2.9990 chunk 497 optimal weight: 0.9980 chunk 277 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 198 optimal weight: 5.9990 chunk 314 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 99 ASN B 205 ASN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 ASN O 209 HIS S 185 ASN U 243 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 49808 Z= 0.282 Angle : 0.524 6.896 67374 Z= 0.285 Chirality : 0.043 0.164 7584 Planarity : 0.004 0.081 8704 Dihedral : 4.981 30.759 6808 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.91 % Allowed : 11.60 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.10), residues: 6180 helix: 1.90 (0.11), residues: 2280 sheet: -0.15 (0.13), residues: 1442 loop : -0.63 (0.12), residues: 2458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 199 HIS 0.006 0.001 HIS O 209 PHE 0.020 0.001 PHE F 179 TYR 0.016 0.001 TYR 1 124 ARG 0.005 0.000 ARG F 51 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12360 Ramachandran restraints generated. 6180 Oldfield, 0 Emsley, 6180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12360 Ramachandran restraints generated. 6180 Oldfield, 0 Emsley, 6180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 441 time to evaluate : 6.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 101 outliers final: 58 residues processed: 516 average time/residue: 2.5655 time to fit residues: 1740.2412 Evaluate side-chains 492 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 434 time to evaluate : 6.178 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 46 residues processed: 13 average time/residue: 1.2240 time to fit residues: 33.2869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 578 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 341 optimal weight: 2.9990 chunk 438 optimal weight: 7.9990 chunk 339 optimal weight: 2.9990 chunk 504 optimal weight: 4.9990 chunk 334 optimal weight: 2.9990 chunk 597 optimal weight: 4.9990 chunk 373 optimal weight: 4.9990 chunk 364 optimal weight: 0.6980 chunk 275 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 99 ASN B 205 ASN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 ASN O 209 HIS S 185 ASN U 243 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 49808 Z= 0.327 Angle : 0.531 6.407 67374 Z= 0.289 Chirality : 0.044 0.179 7584 Planarity : 0.004 0.080 8704 Dihedral : 4.955 30.868 6808 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.85 % Allowed : 11.94 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.10), residues: 6180 helix: 1.91 (0.10), residues: 2282 sheet: -0.21 (0.13), residues: 1492 loop : -0.64 (0.12), residues: 2406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 199 HIS 0.006 0.001 HIS O 209 PHE 0.020 0.002 PHE F 179 TYR 0.016 0.002 TYR 1 124 ARG 0.005 0.000 ARG F 51 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12360 Ramachandran restraints generated. 6180 Oldfield, 0 Emsley, 6180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12360 Ramachandran restraints generated. 6180 Oldfield, 0 Emsley, 6180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 448 time to evaluate : 6.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 98 outliers final: 67 residues processed: 518 average time/residue: 2.5810 time to fit residues: 1750.9589 Evaluate side-chains 499 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 432 time to evaluate : 6.142 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 47 residues processed: 20 average time/residue: 1.2855 time to fit residues: 48.8340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 369 optimal weight: 3.9990 chunk 238 optimal weight: 3.9990 chunk 356 optimal weight: 1.9990 chunk 180 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 115 optimal weight: 9.9990 chunk 379 optimal weight: 0.1980 chunk 407 optimal weight: 2.9990 chunk 295 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 469 optimal weight: 5.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 99 ASN B 205 ASN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 ASN G 243 GLN L 141 HIS O 209 HIS S 185 ASN U 243 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 49808 Z= 0.309 Angle : 0.526 6.788 67374 Z= 0.286 Chirality : 0.044 0.162 7584 Planarity : 0.004 0.079 8704 Dihedral : 4.917 31.065 6808 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.78 % Allowed : 12.43 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.10), residues: 6180 helix: 1.95 (0.10), residues: 2284 sheet: -0.23 (0.13), residues: 1496 loop : -0.65 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 199 HIS 0.006 0.001 HIS O 209 PHE 0.019 0.002 PHE F 179 TYR 0.017 0.001 TYR 1 124 ARG 0.005 0.000 ARG F 51 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12360 Ramachandran restraints generated. 6180 Oldfield, 0 Emsley, 6180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12360 Ramachandran restraints generated. 6180 Oldfield, 0 Emsley, 6180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 451 time to evaluate : 6.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 94 outliers final: 61 residues processed: 518 average time/residue: 2.5092 time to fit residues: 1708.8932 Evaluate side-chains 493 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 432 time to evaluate : 6.205 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 46 residues processed: 15 average time/residue: 1.3070 time to fit residues: 38.4809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 543 optimal weight: 0.9990 chunk 572 optimal weight: 2.9990 chunk 522 optimal weight: 1.9990 chunk 556 optimal weight: 3.9990 chunk 335 optimal weight: 1.9990 chunk 242 optimal weight: 3.9990 chunk 437 optimal weight: 10.0000 chunk 170 optimal weight: 8.9990 chunk 503 optimal weight: 2.9990 chunk 526 optimal weight: 2.9990 chunk 554 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 99 ASN B 205 ASN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 ASN S 185 ASN U 243 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 49808 Z= 0.227 Angle : 0.505 6.457 67374 Z= 0.273 Chirality : 0.043 0.165 7584 Planarity : 0.004 0.079 8704 Dihedral : 4.819 29.802 6808 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.47 % Allowed : 13.02 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.10), residues: 6180 helix: 2.08 (0.11), residues: 2278 sheet: -0.15 (0.13), residues: 1482 loop : -0.58 (0.12), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 199 HIS 0.004 0.001 HIS A 209 PHE 0.019 0.001 PHE R 174 TYR 0.015 0.001 TYR 1 124 ARG 0.004 0.000 ARG F 51 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12360 Ramachandran restraints generated. 6180 Oldfield, 0 Emsley, 6180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12360 Ramachandran restraints generated. 6180 Oldfield, 0 Emsley, 6180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 455 time to evaluate : 6.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 53 residues processed: 514 average time/residue: 2.5321 time to fit residues: 1720.3150 Evaluate side-chains 489 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 436 time to evaluate : 6.202 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 46 residues processed: 7 average time/residue: 1.2956 time to fit residues: 22.0655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 365 optimal weight: 3.9990 chunk 588 optimal weight: 4.9990 chunk 359 optimal weight: 1.9990 chunk 279 optimal weight: 1.9990 chunk 409 optimal weight: 10.0000 chunk 617 optimal weight: 0.0670 chunk 568 optimal weight: 3.9990 chunk 491 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 379 optimal weight: 0.0060 chunk 301 optimal weight: 2.9990 overall best weight: 1.4140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 99 ASN B 205 ASN E 185 ASN G 243 GLN S 185 ASN U 243 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 49808 Z= 0.197 Angle : 0.492 6.456 67374 Z= 0.265 Chirality : 0.043 0.183 7584 Planarity : 0.004 0.080 8704 Dihedral : 4.707 27.371 6808 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.31 % Favored : 97.67 % Rotamer: Outliers : 1.28 % Allowed : 13.45 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.11), residues: 6180 helix: 2.19 (0.11), residues: 2282 sheet: -0.12 (0.13), residues: 1484 loop : -0.48 (0.12), residues: 2414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 199 HIS 0.004 0.001 HIS A 209 PHE 0.020 0.001 PHE R 174 TYR 0.014 0.001 TYR 1 124 ARG 0.004 0.000 ARG F 51 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12360 Ramachandran restraints generated. 6180 Oldfield, 0 Emsley, 6180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12360 Ramachandran restraints generated. 6180 Oldfield, 0 Emsley, 6180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 446 time to evaluate : 6.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 49 residues processed: 501 average time/residue: 2.6008 time to fit residues: 1729.8230 Evaluate side-chains 473 residues out of total 5292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 424 time to evaluate : 6.253 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 43 residues processed: 6 average time/residue: 1.0166 time to fit residues: 18.9014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 620 random chunks: chunk 390 optimal weight: 3.9990 chunk 523 optimal weight: 0.9980 chunk 150 optimal weight: 0.6980 chunk 453 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 chunk 492 optimal weight: 0.6980 chunk 206 optimal weight: 0.9980 chunk 505 optimal weight: 0.9980 chunk 62 optimal weight: 9.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: